The expanding HIV-1 pandemic, and the failure of human efficacy trials of T-cell and antibody-based vaccines, highlight the major gaps in knowledge that must be filled in order to pursue rational HIV-1 vaccine design and development. One of the most important knowledge gaps relates to the precise nature of early virus-host interactions that lead to virus transmission and productive clinical infection. This application is a new HIVRAD proposal by investigators whose recent scientific discoveries relate directly to this priority area of research. These discoveries - the identification of transmitted/founder HIV-1 and SIV genomes (Keele 2008;Keele 2009;Salazar 2009), the identification of genetically-divergent SIVsmm strains in naturally-infected sooty mangabeys (Apetrei 2005;Apetrei 2007), and the identification of innate mucosal immune responses modulating early virus-host interactions (Estes 2006;Estes 2008;Li 2009) - create a unique and timely opportunity to focus three cutting edge research themes on a high priority HIV/SIV vaccine research problem. The current proposal is comprised of three interrelated projects and two cores led by investigators at the University of Alabama at Birmingham (Shaw and Hahn);the University of Pittsburgh (Apetrei and Pandrea);and NCI-Frederick (Estes, Keele and Lifson). Project #1 is "Mucosal transmission and pathogenicity of novel SIVsmm virus strains (Apetrei)." Project #2 is "Identification, cloning and characterization of transmitted/founder SIVsmm (Hahn)." Project #3 is "Molecular analysis of the mucosal SIVsmm transmission bottleneck (Shaw)." Collectively, the projects will test this hypothesis: Identification, molecular cloning, and in vivo analysis of naturally-occurring mucosally-transmitted strains of SIVsmm corresponding to transmitted/founder viruses will reveal viral-host interactions responsible for selective SIV transmission across rectal, vaginal and cervical mucosa and will provide novel, genetically-divergent, pathogenic virus challenge strains for vaccine testing. A key deliverable of this research to the SIV/HIV vaccine field, in addition to new scientific insights into mucosal transmission, will be 18 molecular clones of transmitted/founder viruses representing three widely divergent SIVsmm genetic lineages for use as potential challenge stocks. RELEVANCE: The expanding HIV-1 pandemic, and the failure of human clinical trials of T-cell and antibody-based vaccines, highlight gaps in scientific knowledge about the initial steps in virus transmission and vaccine approaches to prevent infection. This project will identify and clone new, naturally occurring strains of SIVsmm and will use these to elucidate early infection events in the SIV-rhesus macaque model of human HIV-1 infection. PROJECT 1: Title: Mucosal Transmission and Pathogenicity of Novel SIVsmm Virus Strains Project Leader: Apetrei, C PROJECT 1 DESCRIPTION (provided by applicant): The development of an effective AIDS vaccine remains one of the highest priorities in HIV research. Studies of HIV pathogenesis, vaccine design and antiretroviral treatments require an appropriate animal model. However, the existing SIV/macaque model has major limitations since (i) prototypic SIVmac strains are too pathogenic, (ii) do not represent mucosally transmitted viruses, and (iii) have been extensively passaged in vitro and in vivo. We have recently identified a large set of new SIVsmm strains which mirror HIV-1 group M viruses in their genetic diversity. Moreover, preliminary in vivo results show that infection of RMs with these SIVsmm strains more closely reproduces the natural history of HIV-1 in humans. Within this HIVRAD consortium, we thus propose to use these new SIVsmm strains to generate new (molecularly cloned) challenge viruses for AIDS vaccine and pathogenesis studies. Project 1 will use a dose-escalation strategy to infect 21 Indian rhesus macaques (RMs) with genetically diverse SIVsmm strains using intravenous (iv), intrarectal (ir) and intravaginal (ivag) routes. Project 2 will then employ single genome amplification (SGA) techniques to infer, and subsequently clone, transmitted/founder (T/F) virus(es) from all of these animals. Following detailed in vitro characterization, a subset of clones will be selected for in vivo competition (n=18) and pathogenesis (n=8) studies which will be performed by Project 1. Specific Aims include: 1. To generate high titer plasma stocks of genetically divergent SIVsmm strains without in vitro adaptation for subsequent mucosal and intravenous transmission studies. 2. To infect RMs by intravenous, intrarectal and intravaginal routes with physiologically relevant doses of genetically divergent SIVsmm strains to allow for the identification of transmitted founder (T/F) viruses: 3. To identify SIVsmm clones with, preferential mucosal transmissiblity and replication fitness by conducting an in vivo competition experiment. 4. To characterize the selected SIVsmm clones for in vivo replication kinetics, pathogenicity and suitability as vaccine challenge stocks. We expect these studies to generate new infectious molecular clones of SIVs with biological properties that more faithfully recapitulate the transmission, pathogenic and diversity of HIV-1 in humans. RELEVANCE: This project will generate new viral stocks and virological reagents critically needed to elucidate the molecular and cellular events that are responsible for HIV/SIV transmission across rectal and vaginal/cervical mucosa and thus eliminate a major roadblock to AIDS vaccine development.